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Imagery from unoccupied aerial vehicles (UAVs) is useful for mapping floating and emerged primary producers, as well as single taxa of submerged primary producers in shallow, clear lakes and streams. However, there is little research on the effectiveness of UAV imagery-based detection and quantification of submerged filamentous algae and rooted macrophytes in deeper rivers using a standard red-green-blue (RGB) camera. This study provides a novel application of UAV imagery analysis for monitoring a non-wadeable river, the Klamath River in northern California, USA. River depth and solar angle during flight were analyzed to understand their effects on benthic primary producer detection. A supervised, pixel-based Random Trees classifier was utilized as a detection mechanism to estimate the percent cover of submerged filamentous algae and rooted macrophytes from aerial photos within 32 sites along the river in June and July 2019. In-situ surveys conducted via wading and snorkeling were used to validate these data. Overall accuracy was 82% for all sites and the highest overall accuracy of classified UAV images was associated with solar angles between 47.5 and 58.72° (10:04 a.m. to 11:21 a.m.). Benthic algae were detected at depths of 1.9 m underwater and submerged macrophytes were detected down to 1.2 m (river depth) via the UAV imagery in this relatively clear river (Secchi depth &gt; 2 m). Percent cover reached a maximum of 31% for rooted macrophytes and 39% for filamentous algae within all sites. Macrophytes dominated the upstream reaches, while filamentous algae dominated the downstream reaches closer to the Pacific Ocean. In upcoming years, four proposed dam removals are expected to alter the species composition and abundance of benthic filamentous algae and rooted macrophytes, and aerial imagery provides an effective method to monitor these changes.

Application of UAV Imagery to Detect and Quantify Submerged Filamentous Algae and Rooted Macrophytes in a Non-Wadeable River